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Bacterial whole genome sequencing

Li Fang, Qiong Chen, Keren Shi, Xi Li, Qiucheng Shi, Fang He, Jiancang Zhou, Yunsong Yu, Xiaoting Hua
Klebsiella pneumoniae is a gram-negative bacterium that causes numerous diseases, including pneumonia and urinary tract infections. An increase in multidrug resistance has complicated the treatment of these bacterial infections, and although tigecycline shows activity against a broad spectrum of bacteria, resistant strains have emerged. In this study, the whole genomes of two clinical and six laboratory-evolved strains were sequenced to identify putative mutations related to tigecycline resistance. Of seven tigecycline-resistant strains, seven (100%) had ramR mutations, five (71...
2016: PloS One
Philippe Chouvarine, Lutz Wiehlmann, Patricia Moran Losada, David S DeLuca, Burkhard Tümmler
Ever-increasing affordability of next-generation sequencing makes whole-metagenome sequencing an attractive alternative to traditional 16S rDNA, RFLP, or culturing approaches for the analysis of microbiome samples. The advantage of whole-metagenome sequencing is that it allows direct inference of the metabolic capacity and physiological features of the studied metagenome without reliance on the knowledge of genotypes and phenotypes of the members of the bacterial community. It also makes it possible to overcome problems of 16S rDNA sequencing, such as unknown copy number of the 16S gene and lack of sufficient sequence similarity of the "universal" 16S primers to some of the target 16S genes...
2016: PloS One
Brenda Anna Kwambana-Adams, Franklin Asiedu-Bekoe, Badu Sarkodie, Osei Kuffour Afreh, George Khumalo Kuma, Godfred Owusu-Okyere, Ebenezer Foster-Nyarko, Sally-Ann Ohene, Charles Okot, Archibald Kwame Worwui, Catherine Okoi, Madikay Senghore, Jacob Kweku Otu, Chinelo Ebruke, Richard Bannerman, Kwame Amponsa-Achiano, David Opare, Gemma Kay, Timothy Letsa, Owen Kaluwa, Ebenezer Appiah-Denkyira, Victor Bampoe, Syed M A Zaman, Mark J Pallen, Umberto D'Alessandro, Jason M Mwenda, Martin Antonio
BACKGROUND: An outbreak of pneumococcal meningitis among non-infant children and adults occurred in the Brong-Ahafo region of Ghana between December 2015 and April 2016 despite the recent nationwide implementation of a vaccination programme for infants with the 13-valent pneumococcal conjugate vaccine (PCV13). METHODS: Cerebrospinal fluid (CSF) specimens were collected from patients with suspected meningitis in the Brong-Ahafo region. CSF specimens were subjected to Gram staining, culture and rapid antigen testing...
October 18, 2016: BMC Infectious Diseases
Seong-Tshool Hong
The human intestine contains a massive and complex microbial community called gut microbiota. A typical human carries 100 trillion microbes in his/her body which is 10 times greater than the number of their host cells, i.e. whole number of human cells. A combined microbial genome constituting gut microbiota is well excess our own human genome. The microbial composition of gut microbiotata and its role on diseases became a booming area of research, presenting a new paradigm of opportunities for modern medicines...
September 2016: Journal of Hypertension
Marcela Suárez-Esquivel, Nazareth Ruiz-Villalobos, Amanda Castillo-Zeledón, César Jiménez-Rojas, R Martin Roop Ii, Diego J Comerci, Elías Barquero-Calvo, Carlos Chacón-Díaz, Clayton C Caswell, Kate S Baker, Esteban Chaves-Olarte, Nicholas R Thomson, Edgardo Moreno, Jean J Letesson, Xavier De Bolle, Caterina Guzmán-Verri
Brucellosis is a bacterial infectious disease affecting a wide range of mammals and a neglected zoonosis caused by species of the genetically homogenous genus Brucella. As in most studies on bacterial diseases, research in brucellosis is carried out by using reference strains as canonical models to understand the mechanisms underlying host pathogen interactions. We performed whole genome sequencing analysis of the reference strain B. abortus 2308 routinely used in our laboratory, including manual curated annotation accessible as an editable version through a link at https://en...
2016: Frontiers in Microbiology
Ulrich Nübel
Driven by progress of DNA sequencing technologies, recent population genomics studies have revealed that several bacterial pathogens constitute 'measurably evolving populations'. As a consequence, it was possible to reconstruct the emergence and spatial spread of drug-resistant bacteria on the basis of temporally structured samples of bacterial genome sequences. Based on currently available data, some general inferences can be drawn across different bacterial species as follows: (1) Resistance to various antibiotics evolved years to decades earlier than had been anticipated on the basis of epidemiological surveillance data alone...
October 15, 2016: Current Topics in Microbiology and Immunology
A Miglio, V Stefanetti, M T Antognoni, K Cappelli, S Capomaccio, M Coletti, F Passamonti
BACKGROUND: Bacterial contamination of whole blood (WB) units can result in transfusion-transmitted infection, but the extent of the risk has not been established and may be underestimated in veterinary medicine. OBJECTIVES: To detect, quantify, and identify bacterial microorganisms in 49 canine WB units during their shelf life. ANIMALS: Forty-nine healthy adult dogs. METHODS: Forty-nine WB units were included in the study...
October 13, 2016: Journal of Veterinary Internal Medicine
Melissa J Jansen van Rensburg, Craig Swift, Alison J Cody, Claire Jenkins, Martin C J Maiden
The application of whole-genome sequencing (WGS) to problems in clinical microbiology has had a major impact on the field. Clinical laboratories are now using WGS for pathogen identification, antimicrobial susceptibility testing, and epidemiological typing. WGS data also represents a valuable resource for the development and evaluation of molecular diagnostic assays, which continue to play an important role in clinical microbiology. To demonstrate this application of WGS, the current study used publicly available genomic data to evaluate a duplex real-time PCR (RT-PCR) assay that targets mapA and ceuE for the detection of Campylobacter jejuni and Campylobacter coli, leading global causes of bacterial gastroenteritis...
October 12, 2016: Journal of Clinical Microbiology
Thomas Brown, Xavier Didelot, Daniel J Wilson, Nicola De Maio
Bacteria can exchange genetic material, or acquire genes found in the environment. This process, generally known as bacterial recombination, can have a strong impact on the evolution and phenotype of bacteria, for example causing the spread of antibiotic resistance across clades and species, but can also disrupt phylogenetic and transmission inferences. With the increasing affordability of whole genome sequencing, the need has emerged for an efficient simulator of bacterial evolution to test and compare methods for phylogenetic and population genetic inference, and for simulation-based estimation...
January 19, 2016: Microbial Genomics
Fabian Lorenzo-Diaz, Cris Fernández-Lopez, Pierre-Emmanuel Douarre, Adrian Baez-Ortega, Carlos Flores, Philippe Glaser, Manuel Espinosa
Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance...
October 2016: Open Biology
Jeong-Sun Seo, Arang Rhie, Junsoo Kim, Sangjin Lee, Min-Hwan Sohn, Chang-Uk Kim, Alex Hastie, Han Cao, Ji-Young Yun, Jihye Kim, Junho Kuk, Gun Hwa Park, Juhyeok Kim, Hanna Ryu, Jongbum Kim, Mira Roh, Jeonghun Baek, Michael W Hunkapiller, Jonas Korlach, Jong-Yeon Shin, Changhoon Kim
Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17...
October 5, 2016: Nature
Ana M Misic, Christine L Cain, Daniel O Morris, Shelley C Rankin, Daniel P Beiting
Staphylococcus species are a leading cause of skin and soft tissue infections in humans and animals, and the antibiotics used to treat these infections are often the same. Methicillin- and multidrug-resistant staphylococcal infections are becoming more common in human and veterinary medicine. From a "One Health" perspective, this overlap in antibiotic use and resistance raises concerns over the potential spread of antibiotic resistance genes. Whole-genome sequencing and comparative genomics analysis revealed that Staphylococcus species use divergent pathways to synthesize isoprenoids...
September 2016: MSphere
Patricia Morán Losada, Burkhard Tümmler
Genomic sequence diversity of a bacterial species mainly results from the frequency distribution of single nucleotide polymorphisms (SNPs). Here we report on a SNP-matrix based binary algorithm to determine the intra- or interclonal genomic diversity by the number of shared sequential SNPs, the so-called SNP synteny or haplotype. All SNP positions and the frequency and length distribution of haplotypes are determined from pairwise alignment of completely sequenced genomes. This metric is invariant regarding the reference genome chosen...
October 3, 2016: FEMS Microbiology Letters
Nicholas Jochumsen, Rasmus L Marvig, Søren Damkiær, Rune Lyngklip Jensen, Wilhelm Paulander, Søren Molin, Lars Jelsbak, Anders Folkesson
Colistin is an antimicrobial peptide that has become the only remaining alternative for the treatment of multidrug-resistant Gram-negative bacterial infections, but little is known of how clinical levels of colistin resistance evolve. We use in vitro experimental evolution and whole-genome sequencing of colistin-resistant Pseudomonas aeruginosa isolates from cystic fibrosis patients to reconstruct the molecular evolutionary pathways open for high-level colistin resistance. We show that the evolution of resistance is a complex, multistep process that requires mutation in at least five independent loci that synergistically create the phenotype...
October 3, 2016: Nature Communications
Peter E Burby, Taylor M Nye, Jeremy W Schroeder, Lyle A Simmons
Few discoveries have been more transformative to the biological sciences than the development of DNA sequencing technologies. The rapid advancement of sequencing and bioinformatics tools has revolutionized bacterial genetics, deepening our understanding of model and clinically relevant organisms. Although application of newer sequencing technologies to studies in bacterial genetics is increasing, the implementation of DNA sequencing technologies and development of the bioinformatics tools required for analyzing the large data sets generated remains a challenge for many...
September 26, 2016: Journal of Bacteriology
Andrew McDowell, Emma Barnard, Jared Liu, Huiying Li, Sheila Patrick
Recently, strains of Propionibacterium acnes from the type III genetic division have been proposed as Propionibacterium acnes subsp. elongatum subsp. nov., with strains from the type I and II divisions collectively classified as Propionibacterium acnes subsp. acnes subsp. nov. Under such a taxonomic re-appraisal, we believe that types I and II should also have their own separate rank of subspecies. In support of this, we describe a polyphasic taxonomic study based on the analysis of publically available multilocus and whole genome sequence datasets, alongside a systematic review of previously published phylogenetic, genomic, phenotypic and clinical data...
September 25, 2016: International Journal of Systematic and Evolutionary Microbiology
Crystal J Jaing, Kevin S McLoughlin, James B Thissen, Adam Zemla, Shea N Gardner, Lisa M Vergez, Feliza Bourguet, Shalini Mabery, Viacheslav Y Fofanov, Heather Koshinsky, Paul J Jackson
Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, provide better treatment options for patients...
2016: PloS One
Emmanuel Andre, Léonie Goeminne, Andrea M Cabibbe, Patrick Beckert, Benoît Kabamba Mukadi, Vanessa Mathys, Sébastien Gagneux, Stefan Niemann, Jakko Van Ingen, Emmanuelle Cambau
The rpoB gene codes for the RNA polymerase β subunit, which is the target of rifampicin, an essential drug in the treatment of tuberculosis and other mycobacterial infections. This gene is present in all bacteria, but its length and nucleotide sequence vary between bacterial species, including mycobacteria Mutations in the rpoB gene alter the structure of this protein and cause drug resistance. To describe the resistance-associated mutations, the scientific and medical communities have been using since 1993, a numbering system based on the Escherichia coli sequence annotation...
September 21, 2016: Clinical Microbiology and Infection
C J Anderson, W T Tay, A McGaughran, K Gordon, T K Walsh
Helicoverpa armigera is a major agricultural pest that is distributed across Europe, Asia, Africa and Australasia. This species is hypothesized to have spread to the Americas 1.5 million years ago, founding a population that is at present, a distinct species, Helicoverpa zea. In 2013, H. armigera was confirmed to have re-entered South America via Brazil and subsequently spread. The source of the recent incursion is unknown and population structure in H. armigera is poorly resolved, but a basic understanding would highlight potential biosecurity failures and determine the recent evolutionary history of region-specific lineages...
September 23, 2016: Molecular Ecology
Samantha M Gromek, Andrea M Suria, Matthew S Fullmer, Jillian L Garcia, Johann Peter Gogarten, Spencer V Nyholm, Marcy J Balunas
Female members of many cephalopod species house a bacterial consortium in the accessory nidamental gland (ANG), part of the reproductive system. These bacteria are deposited into eggs that are then laid in the environment where they must develop unprotected from predation, pathogens, and fouling. In this study, we characterized the genome and secondary metabolite production of Leisingera sp. JC1, a member of the roseobacter clade (Rhodobacteraceae) of Alphaproteobacteria isolated from the jelly coat of eggs from the Hawaiian bobtail squid, Euprymna scolopes...
2016: Frontiers in Microbiology
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